Synthetic hyperacetylation of nucleosomal histones

Kajino, Hidetoshi; Nagatani, Tomomi; Oi, Miku; Kujirai, Tomoya; Kurumizaka, Hitoshi; Nishiyama, Atsuya; Nakanishi, Makoto; Yamatsugu, Kenzo; Kawashima, Shinichi; Kanai, Motomu

doi:10.1039/d0cb00029a

Cited by 14 publications

(20 citation statements)

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“…Colocalization of a catalyst for the acylation reaction (4‐(dimethylamino)pyridine, DMAP) further enhanced the selectivity and yield of the acylation reaction with either acetyl or malonyl PTMs (Figure 6). Recently a more effective acyl donor system was identified which performs the acylation reaction only in the presence of the catalyst providing further enhanced selectivity [90] . These artificial acylation systems result in hyperacetylation of histone tails with no site selectivity, limiting their utility to study the complex histone code, but are nevertheless useful tools and present a promising avenue for further exploration towards chemical editing of histone acylation.…”

Section: Lysine Post‐translational Modificationsmentioning

confidence: 99%

Advances and Opportunities in Epigenetic Chemical Biology

2020

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The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally , we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.

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Section: Lysine Post‐translational Modificationsmentioning

confidence: 99%

Advances and Opportunities in Epigenetic Chemical Biology

2020

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“…In these bioconjugation methods, the ligand leaves the active site after forming a covalent bond with a nucleophilic residue on the POI . Although these methods enabled prominent applications and could retain target protein activity, , some challenges remain. First, the size of the required activating groups and/or linkers is substantial and precludes the labeling of residues very close to the active site.…”

Section: Introductionmentioning

confidence: 99%

Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry

et al. 2021

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Chemical modifications of native proteins can affect their stability, activity, interactions, localization, and more. However, there are few nongenetic methods for the installation of chemical modifications at a specific protein site in cells. Here we report a covalent ligand directed release (CoLDR) site-specific labeling strategy, which enables the installation of a variety of functional tags on a target protein while releasing the directing ligand. Using this approach, we were able to label various proteins such as BTK, K-Ras G12C , and SARS-CoV-2 PL pro with different tags. For BTK we have shown selective labeling in cells of both alkyne and fluorophores tags. Protein labeling by traditional affinity methods often inhibits protein activity since the directing ligand permanently occupies the target binding pocket. We have shown that using CoLDR chemistry, modification of BTK by these probes in cells preserves its activity. We demonstrated several applications for this approach including determining the half-life of BTK in its native environment with minimal perturbation, as well as quantification of BTK degradation by a noncovalent proteolysis targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive "turn-on" fluorescent probe, we were able to monitor ligand binding to the active site of BTK. Finally, we have demonstrated efficient CoLDR-based BTK PROTACs (DC 50 < 100 nM), which installed a CRBN binder onto BTK. This approach joins very few available labeling strategies that maintain the target protein activity and thus makes an important addition to the toolbox of chemical biology.

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“…The DMAP moiety of the catalyst activates the acetyl donor to generate an acetyl pyridinium ion intermediate, the active species promoting acetylation of proximate lysine residues on histone tails. Interestingly, synthetic histone acetylation of Xenopus chromatin by 16DMAP with PAc-gly prevented DNA replication in cell-free Xenopus egg extract system, providing a novel link between histone acetylation and cell cycle (12). However, oligoDMAP-based catalysts did not work in live cells, probably due to inactivation of the catalytically active species (i.e., acetyl pyridinium ion) under highly reductive and nucleophilic environment in cells (e.g., the presence of glutathione [GSH]) (13).…”

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confidence: 99%

“…So far, two chemical catalyst systems to directly modify histones in nucleosomes have been reported. The first catalyst system is composed of an oligoDMAPbased catalyst (DMAP: 4-dimethylaminopyridine), such as 8DMAP or 16DMAP, and an acetyl donor, such as an N-methoxydiacetamide derivative or a phenyl acetate-derivative (PAc-gly) (10,12). These oligocationic catalysts bind to nucleosomes through electrostatic interactions with negatively charged DNA.…”

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confidence: 99%

Live-cell epigenome manipulation by synthetic histone acetylation catalyst system

Fujiwara

Yamanashi

Fujimura

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Chemical modifications of histones, such as lysine acetylation and ubiquitination, play pivotal roles in epigenetic regulation of gene expression. Methods to alter the epigenome thus hold promise as tools for elucidating epigenetic mechanisms and as therapeutics. However, an entirely chemical method to introduce histone modifications in living cells without genetic manipulation is unprecedented. Here, we developed a chemical catalyst, PEG-LANA-DSSMe 11, that binds with nucleosome’s acidic patch and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells. The size of polyethylene glycol in the catalyst was a critical determinant for its in-cell metabolic stability, binding affinity to histones, and high activity. The synthetic acetylation promoted by 11 without genetic manipulation competed with and suppressed physiological H2B ubiquitination, a mark regulating chromatin functions, such as transcription and DNA damage response. Thus, the chemical catalyst will be a useful tool to manipulate epigenome for unraveling epigenetic mechanisms in living cells.

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Synthetic hyperacetylation of nucleosomal histones

Abstract: A chemical catalyst system enabling high-yielding and comprehensive lysine acetylation of nucleosomal histones was developed as an epigenetics tool.

Cited by 14 publications

References 20 publications

Advances and Opportunities in Epigenetic Chemical Biology

Advances and Opportunities in Epigenetic Chemical Biology

Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry

Live-cell epigenome manipulation by synthetic histone acetylation catalyst system

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